1
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Cho SG, Kim JH, Lee JE, Choi IJ, Song M, Chuon K, Shim JG, Kang KW, Jung KH. Heliorhodopsin-mediated light-modulation of ABC transporter. Nat Commun 2024; 15:4306. [PMID: 38773114 PMCID: PMC11109279 DOI: 10.1038/s41467-024-48650-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Heliorhodopsins (HeRs) have been hypothesized to have widespread functions. Recently, the functions for few HeRs have been revealed; however, the hypothetical functions remain largely unknown. Herein, we investigate light-modulation of heterodimeric multidrug resistance ATP-binding cassette transporters (OmrDE) mediated by Omithinimicrobium cerasi HeR. In this study, we classifiy genes flanking the HeR-encoding genes and identify highly conservative residues for protein-protein interactions. Our results reveal that the interaction between OcHeR and OmrDE shows positive cooperatively sequential binding through thermodynamic parameters. Moreover, light-induced OcHeR upregulates OmrDE drug transportation. Hence, the binding may be crucial to drug resistance in O. cerasi as it survives in a drug-containing habitat. Overall, we unveil a function of HeR as regulatory rhodopsin for multidrug resistance. Our findings suggest potential applications in optogenetic technology.
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Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul, South Korea
- Research Institute for Basic Science, Sogang University, Seoul, South Korea
| | - Ji-Hyun Kim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Ji-Eun Lee
- Department of Life Science, Sogang University, Seoul, South Korea
| | - In-Jung Choi
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Myungchul Song
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kimleng Chuon
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Jin-Gon Shim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kun-Wook Kang
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul, South Korea.
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2
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Lyon SE, Wencker FDR, Fernando CM, Harris KA, Breaker RR. Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources. PNAS NEXUS 2024; 3:pgae075. [PMID: 38415217 PMCID: PMC10898510 DOI: 10.1093/pnasnexus/pgae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Ornate, large, extremophilic (OLE) RNAs comprise a class of large noncoding RNAs in bacteria whose members form a membrane-associated ribonucleoprotein (RNP) complex. This complex facilitates cellular adaptation to diverse stresses such as exposure to cold, short-chain alcohols, and elevated Mg2+ concentrations. Here, we report additional phenotypes exhibited by Halalkalibacterium halodurans (formerly called Bacillus halodurans) strains lacking functional OLE RNP complexes. Genetic disruption of the complex causes restricted growth compared to wild-type cells when cultured in minimal media (MM) wherein glucose is replaced with alternative carbon/energy sources. Genetic suppressor selections conducted in glutamate MM yielded isolates that carry mutations in or near genes relevant to Mn2+ homeostasis (ykoY and mntB), phosphate homeostasis (phoR), and putative multidrug resistance (bmrCD). These functional links between OLE RNA, carbon/energy management, and other fundamental processes including protein secretion are consistent with the hypothesis that the OLE RNP complex is a major contributor to cellular adaptation to unfavorable growth conditions.
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Affiliation(s)
- Seth E Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Freya D R Wencker
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
| | - Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Kimberly A Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
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3
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Bohorquez LC, de Sousa J, Garcia-Garcia T, Dugar G, Wang B, Jonker MJ, Noirot-Gros MF, Lalk M, Hamoen LW. Metabolic and chromosomal changes in a Bacillus subtilis whiA mutant. Microbiol Spectr 2023; 11:e0179523. [PMID: 37916812 PMCID: PMC10714963 DOI: 10.1128/spectrum.01795-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE WhiA is a conserved DNA-binding protein that influences cell division in many Gram-positive bacteria and, in B. subtilis, also chromosome segregation. How WhiA works in Bacillus subtilis is unknown. Here, we tested three hypothetical mechanisms using metabolomics, fatty acid analysis, and chromosome confirmation capture experiments. This revealed that WhiA does not influence cell division and chromosome segregation by modulating either central carbon metabolism or fatty acid composition. However, the inactivation of WhiA reduces short-range chromosome interactions. These findings provide new avenues to study the molecular mechanism of WhiA in the future.
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Affiliation(s)
- Laura C. Bohorquez
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Joana de Sousa
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Transito Garcia-Garcia
- Laboratoire de Genetique Microbienne, Domaine de Vilvert, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Gaurav Dugar
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Biwen Wang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Martijs J. Jonker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marie-Françoise Noirot-Gros
- Laboratoire de Genetique Microbienne, Domaine de Vilvert, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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4
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Deves V, Trinquier A, Gilet L, Alharake J, Condon C, Braun F. Shutdown of multidrug transporter bmrCD mRNA expression mediated by the ribosome-associated endoribonuclease (Rae1) cleavage in a new cryptic ORF. RNA (NEW YORK, N.Y.) 2023; 29:1108-1116. [PMID: 37142436 PMCID: PMC10351889 DOI: 10.1261/rna.079692.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023]
Abstract
Rae1 is a well-conserved endoribonuclease among Gram-positive bacteria, cyanobacteria, and the chloroplasts of higher plants. We have previously shown that Rae1 cleaves the Bacillus subtilis yrzI operon mRNA in a translation-dependent manner within a short open reading frame (ORF) called S1025, encoding a 17-amino acid (aa) peptide of unknown function. Here, we map a new Rae1 cleavage site in the bmrBCD operon mRNA encoding a multidrug transporter, within an unannotated 26-aa cryptic ORF that we have named bmrX Expression of the bmrCD portion of the mRNA is ensured by an antibiotic-dependent ribosome attenuation mechanism within the upstream ORF bmrB Cleavage by Rae1 within bmrX suppresses bmrCD expression that escapes attenuation control in the absence of antibiotics. Similar to S1025, Rae1 cleavage within bmrX is both translation- and reading frame-dependent. Consistent with this, we show that translation-dependent cleavage by Rae1 promotes ribosome rescue by the tmRNA.
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Affiliation(s)
- Valentin Deves
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Aude Trinquier
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Laetitia Gilet
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jawad Alharake
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Ciarán Condon
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Frédérique Braun
- Expression Génétique Microbienne (EGM), CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
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5
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Guidi F, Lorenzetti C, Centorotola G, Torresi M, Cammà C, Chiaverini A, Pomilio F, Blasi G. Atypical Serogroup IVb-v1 of Listeria monocytogenes Assigned to New ST2801, Widely Spread and Persistent in the Environment of a Pork-Meat Producing Plant of Central Italy. Front Microbiol 2022; 13:930895. [PMID: 35832815 PMCID: PMC9271897 DOI: 10.3389/fmicb.2022.930895] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we characterized 84 Listeria monocytogenes (Lm) strains having an atypical IVb-v1 profile and isolated in a meat producing plant of Central Italy. They were assigned to the new MLST type ST2801 (CC218). The new ST was widespread in the food-producing environment where it was able to persist for over a year even after cleaning and sanitation. Cluster analysis identified three main clusters genetically close to each other (0-22 allelic differences and 0-28 SNPs) from two different cgMLST types, suggesting a common source. The coexistence of closely related clusters over time could be the result of a different evolution path starting from a common ancestor first introduced in the plant and/or the consequence of the repetitive reintroduction of closely related clones probably by raw materials. All the strains presented several determinants for heavy metals resistance, stress response, biofilm production, and multidrug efflux pumps with no significant differences among the clusters. A total of 53 strains carried pLI100 and the j1776 plasmids, while in one strain, the pLM33 was found in addition to pLI100. Only the strains carrying plasmids presented cadA and cadC for cadmium resistance and the mco gene encoding a multicopper oxidase and gerN for an additional Na+/H+-K+ antiporter. All the strains presented a virulence profile including a full-length inlA gene and the additional LIPI-3. The isolation of a new ST with a large pattern of stress-adaptation genes and able to persist is an important contribution to deepening the current knowledge on the uncommon IVb-v1 and in general on the genomic diversity of Lm.
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Affiliation(s)
- Fabrizia Guidi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati,” Perugia, Italy
| | - Cinzia Lorenzetti
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati,” Perugia, Italy
| | - Gabriella Centorotola
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Marina Torresi
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Cesare Cammà
- Centro di Referenza Nazionale per Sequenze Genomiche di Microrganismi Patogeni, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Alexandra Chiaverini
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Francesco Pomilio
- Laboratorio Nazionale di Riferimento per Listeria Monocytogenes, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, Teramo, Italy
| | - Giuliana Blasi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati,” Perugia, Italy
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6
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Thaker TM, Mishra S, Zhou W, Mohan M, Tang Q, Faraldo-Goméz JD, Mchaourab HS, Tomasiak TM. Asymmetric drug binding in an ATP-loaded inward-facing state of an ABC transporter. Nat Chem Biol 2022; 18:226-235. [PMID: 34931066 PMCID: PMC9242650 DOI: 10.1038/s41589-021-00936-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/26/2021] [Indexed: 12/24/2022]
Abstract
Substrate efflux by ATP-binding cassette (ABC) transporters, which play a major role in multidrug resistance, entails the ATP-powered interconversion between transporter intermediates. Despite recent progress in structure elucidation, a number of intermediates have yet to be visualized and mechanistically interpreted. Here, we combine cryogenic-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy and molecular dynamics simulations to profile a previously unobserved intermediate of BmrCD, a heterodimeric multidrug ABC exporter from Bacillus subtilis. In our cryo-EM structure, ATP-bound BmrCD adopts an inward-facing architecture featuring two molecules of the substrate Hoechst-33342 in a striking asymmetric head-to-tail arrangement. Deletion of the extracellular domain capping the substrate-binding chamber or mutation of Hoechst-coordinating residues abrogates cooperative stimulation of ATP hydrolysis. Together, our findings support a mechanistic role for symmetry mismatch between the nucleotide binding and the transmembrane domains in the conformational cycle of ABC transporters and is of notable importance for rational design of molecules for targeted ABC transporter inhibition.
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Affiliation(s)
- Tarjani M Thaker
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- St Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Mohan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Qingyu Tang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - José D Faraldo-Goméz
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.
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7
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Roche B, Garcia-Rivera MA, Normant V, Kuhn L, Hammann P, Brönstrup M, Mislin GLA, Schalk IJ. A role for PchHI as the ABC transporter in iron acquisition by the siderophore pyochelin in Pseudomonas aeruginosa. Environ Microbiol 2021; 24:866-877. [PMID: 34664350 DOI: 10.1111/1462-2920.15811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022]
Abstract
Iron is an essential nutrient for bacterial growth but poorly bioavailable. Bacteria scavenge ferric iron by synthesizing and secreting siderophores, small compounds with a high affinity for iron. Pyochelin (PCH) is one of the two siderophores produced by the opportunistic pathogen Pseudomonas aeruginosa. After capturing a ferric iron molecule, PCH-Fe is imported back into bacteria first by the outer membrane transporter FptA and then by the inner membrane permease FptX. Here, using molecular biology, 55 Fe uptake assays, and LC-MS/MS quantification, we first find a role for PchHI as the heterodimeric ABC transporter involved in the siderophore-free iron uptake into the bacterial cytoplasm. We also provide the first evidence that PCH is able to reach the bacterial periplasm and cytoplasm when both FptA and FptX are expressed. Finally, we detected an interaction between PchH and FptX, linking the ABC transporter PchHI with the inner permease FptX in the PCH-Fe uptake pathway. These results pave the way for a better understanding of the PCH siderophore pathway, giving future directions to tackle P. aeruginosa infections.
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Affiliation(s)
- Béatrice Roche
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
| | - Mariel A Garcia-Rivera
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, 38124, Germany
| | - Vincent Normant
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 2 allée Konrad Roentgen, Strasbourg Cedex, F-67084, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 2 allée Konrad Roentgen, Strasbourg Cedex, F-67084, France
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, 38124, Germany
| | - Gaëtan L A Mislin
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
| | - Isabelle J Schalk
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France.,Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67412, France
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8
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Pipatthana M, Harnvoravongchai P, Pongchaikul P, Likhitrattanapisal S, Phanchana M, Chankhamhaengdecha S, Janvilisri T. The repertoire of ABC proteins in Clostridioides difficile. Comput Struct Biotechnol J 2021; 19:2905-2920. [PMID: 34094001 PMCID: PMC8144104 DOI: 10.1016/j.csbj.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 11/07/2022] Open
Abstract
ABC transporters transport substrates across membranes driven by ATP hydrolysis. ABC proteins of C. difficile 630 can be classified into 12 sub-families. Most NPs are found within sub-families involving in drug export. Most core NPs in C. difficile are associated with drug efflux system. ABC proteins in sub-families 3, 6, 7, and 9 may participate in drug resistance.
ATP-binding cassette (ABC) transporters belong to one of the largest membrane protein superfamilies, which function in translocating substrates across biological membranes using energy from ATP hydrolysis. Currently, the classification of ABC transporters in Clostridioides difficile is not complete. Therefore, the sequence-function relationship of all ABC proteins encoded within the C. difficile genome was analyzed. Identification of protein domains associated with the ABC system in the C. difficile 630 reference genome revealed 226 domains: 97 nucleotide-binding domains (NBDs), 98 transmembrane domains (TMDs), 30 substrate-binding domains (SBDs), and one domain with features of an adaptor protein. Gene organization and transcriptional unit analyses indicated the presence of 78 ABC systems comprising 28 importers and 50 exporters. Based on NBD sequence similarity, ABC transporters were classified into 12 sub-families according to their substrates. Interestingly, all ABC exporters, accounting for 64% of the total ABC systems, are involved in antibiotic resistance. Based on analysis of ABC proteins from 49 C. difficile strains, the majority of core NBDs are predicted to be involved in multidrug resistance systems, consistent with the ability of this organism to survive exposure to an array of antibiotics. Our findings herein provide another step toward a better understanding of the function and evolutionary relationships of ABC proteins in this pathogen.
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Affiliation(s)
- Methinee Pipatthana
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakarn, Thailand
| | - Somsak Likhitrattanapisal
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
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9
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Wex KW, Saur JS, Handel F, Ortlieb N, Mokeev V, Kulik A, Niedermeyer THJ, Mast Y, Grond S, Berscheid A, Brötz-Oesterhelt H. Bioreporters for direct mode of action-informed screening of antibiotic producer strains. Cell Chem Biol 2021; 28:1242-1252.e4. [PMID: 33761329 DOI: 10.1016/j.chembiol.2021.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/27/2021] [Accepted: 02/23/2021] [Indexed: 01/17/2023]
Abstract
A big challenge in natural product research of today is rapid dereplication of already known substances, to free capacities for the exploration of new agents. Prompt information on bioactivities and mode of action (MOA) speeds up the lead discovery process and is required for rational compound optimization. Here, we present a bioreporter approach as a versatile strategy for combined bioactivity- and MOA-informed primary screening for antimicrobials. The approach is suitable for directly probing producer strains grown on agar, without need for initial compound enrichment or purification, and works along the entire purification pipeline with culture supernatants, extracts, fractions, and pure substances. The technology allows for MOA-informed purification to selectively prioritize activities of interest. In combination with high-resolution mass spectrometry, the biosensor panel is an efficient and sensitive tool for compound deconvolution. Concomitant information on the affected metabolic pathway enables the selection of appropriate follow-up assays to elucidate the molecular target.
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Affiliation(s)
- Katharina W Wex
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Julian S Saur
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Franziska Handel
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Nico Ortlieb
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Vladislav Mokeev
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Timo H J Niedermeyer
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department of Pharmaceutical Biology/Pharmacognosy Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Sachsen-Anhalt 06120, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Yvonne Mast
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Niedersachsen 38124, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Stephanie Grond
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany.
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10
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Rismondo J, Schulz LM. Not Just Transporters: Alternative Functions of ABC Transporters in Bacillus subtilis and Listeria monocytogenes. Microorganisms 2021; 9:microorganisms9010163. [PMID: 33450852 PMCID: PMC7828314 DOI: 10.3390/microorganisms9010163] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 12/24/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are usually involved in the translocation of their cognate substrates, which is driven by ATP hydrolysis. Typically, these transporters are required for the import or export of a wide range of substrates such as sugars, ions and complex organic molecules. ABC exporters can also be involved in the export of toxic compounds such as antibiotics. However, recent studies revealed alternative detoxification mechanisms of ABC transporters. For instance, the ABC transporter BceAB of Bacillus subtilis seems to confer resistance to bacitracin via target protection. In addition, several transporters with functions other than substrate export or import have been identified in the past. Here, we provide an overview of recent findings on ABC transporters of the Gram-positive organisms B. subtilis and Listeria monocytogenes with transport or regulatory functions affecting antibiotic resistance, cell wall biosynthesis, cell division and sporulation.
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11
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Feng Z, Liu D, Liu Z, Liang Y, Wang Y, Liu Q, Liu Z, Zang Z, Cui Y. Cloning and Functional Characterization of Putative Escherichia coli ABC Multidrug Efflux Transporter YddA. J Microbiol Biotechnol 2020; 30:982-995. [PMID: 32347079 PMCID: PMC9728188 DOI: 10.4014/jmb.2003.03003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
A putative multidrug efflux gene, yddA, was cloned from the Escherichia coli K-12 strain. A drugsensitive strain of E. coli missing the main multidrug efflux pump AcrB was constructed as a host and the yddA gene was knocked out in wild-type (WT) and drug-sensitive E. coliΔacrB to study the yddA function. Sensitivity to different substrates of WT E.coli, E. coliΔyddA, E. coliΔacrB and E. coliΔacrBΔyddA strains was compared with minimal inhibitory concentration (MIC) assays and fluorescence tests. MIC assay and fluorescence test results showed that YddA protein was a multidrug efflux pump that exported multiple substrates. Three inhibitors, ortho-vanadate, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and reserpine, were used in fluorescence tests. Ortho-vanadate and reserpine significantly inhibited the efflux and increased accumulation of ethidium bromide and norfloxacin, while CCCP had no significant effect on YddA-regulated efflux. The results indicated that YddA relies on energy released from ATP hydrolysis to transfer the substrates and YddA is an ABC-type multidrug exporter. Functional study of unknown ATP-binding cassette (ABC) superfamily transporters in the model organism E. coli is conducive to discovering new multidrug resistance-reversal targets and providing references for studying other ABC proteins of unknown function.
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Affiliation(s)
- Zhenyue Feng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Ziwen Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yimin Liang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Qingpeng Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yudong Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,Corresponding author Phone/Fax: +459-6031177 E-mail:
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12
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Sun C, Chen L, Shen Z. Mechanisms of gastrointestinal microflora on drug metabolism in clinical practice. Saudi Pharm J 2019; 27:1146-1156. [PMID: 31885474 PMCID: PMC6921184 DOI: 10.1016/j.jsps.2019.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/28/2019] [Indexed: 02/06/2023] Open
Abstract
Considered as an essential "metabolic organ", intestinal microbiota plays a key role in human health and the predisposition to diseases. It is an aggregate genome of trillions of microorganisms residing in the human gastrointestinal tract. Since the 20th century, researches have showed that intestinal microbiome possesses a variety of metabolic activities that are able to modulate the fate of more than 30 approved drugs and immune checkpoint inhibitors. These drugs are transformed to bioactive, inactive, or toxic metabolites by microbial direct action or host-microbial co-metabolism. These metabolites are responsible for therapeutic effects exerted by these drugs or side effects induced by these drugs, even for death. In view of the significant effect on the drugs metabolism by the gut microbiota, it is pivotal for personalized medicine to explore additional drugs affected by gut microbiota and their involved strains for further making mechanism clear through suitable animal models. This review mainly focus on specific mechanisms involved, with reference to the current literature about drugs metabolism by related bacteria or its enzymes available.
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Affiliation(s)
- Chaonan Sun
- Department of Dermatology, Institute of Dermatology and Venereology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, Sichuan, 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Ling Chen
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, 410042, China
| | - Zhu Shen
- Department of Dermatology, Institute of Dermatology and Venereology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, Sichuan, 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
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13
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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14
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Avci FG, Atas B, Aksoy CS, Kurpejovic E, Gulsoy Toplan G, Gurer C, Guillerminet M, Orelle C, Jault JM, Sariyar Akbulut B. Repurposing bioactive aporphine alkaloids as efflux pump inhibitors. Fitoterapia 2019; 139:104371. [PMID: 31629051 DOI: 10.1016/j.fitote.2019.104371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 01/13/2023]
Abstract
Extrusion of drugs or drug-like compounds through bacterial efflux pumps is a serious health issue that leads to loss in drug efficacy. Combinatorial therapies of low-efficacy drugs with efflux pump inhibitors may help to restore the activities of such drugs. In this quest, natural products are attractive molecules, since in addition to their wide range of bioactivities they may inhibit efflux pumps. The current work repurposed the bioactive alkaloid roemerine as a potential efflux pump inhibitor. In Bacillus subtilis, both Bmr and BmrA, belonging to the major facilitator and the ATP-binding cassette superfamilies, respectively, were found to be inhibited by roemerine. Scanning electron microscopy and RNA-Seq analyses showed that it potentiated the effect of berberine. Growth rates and checkerboard assays confirmed the synergy of roemerine and berberine and that roemerine prevented berberine efflux by inhibiting Bmr. Transport assays with inverted membrane vesicles prepared from Escherichia coli overexpressing BmrA showed that increasing roemerine concentration decreased the transport of doxorubicin, the BmrA substrate, confirming that roemerine may also be considered as an inhibitor of BmrA. Thus, these findings suggest that conjugation of roemerine to substrates of efflux pumps, Bmr and BmrA, may help to potentiate the activity of their drug substrates.
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Affiliation(s)
- Fatma Gizem Avci
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey.
| | - Basak Atas
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey.
| | - Cemile Selin Aksoy
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey
| | - Eldin Kurpejovic
- Department of Bioengineering, Marmara University, 34722 Kadikoy, Istanbul, Turkey
| | - Gizem Gulsoy Toplan
- Department of Pharmacognosy, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
| | - Caglayan Gurer
- Department of Pharmacognosy, Faculty of Pharmacy, Istanbul University, Istanbul, Turkey.
| | - Maxime Guillerminet
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367 Lyon, France.
| | - Cedric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367 Lyon, France.
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367 Lyon, France.
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15
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Orelle C, Durmort C, Mathieu K, Duchêne B, Aros S, Fenaille F, André F, Junot C, Vernet T, Jault JM. A multidrug ABC transporter with a taste for GTP. Sci Rep 2018; 8:2309. [PMID: 29396536 PMCID: PMC5797166 DOI: 10.1038/s41598-018-20558-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/19/2018] [Indexed: 01/26/2023] Open
Abstract
During the evolution of cellular bioenergetics, many protein families have been fashioned to match the availability and replenishment in energy supply. Molecular motors and primary transporters essentially need ATP to function while proteins involved in cell signaling or translation consume GTP. ATP-Binding Cassette (ABC) transporters are one of the largest families of membrane proteins gathering several medically relevant members that are typically powered by ATP hydrolysis. Here, a Streptococcus pneumoniae ABC transporter responsible for fluoroquinolones resistance in clinical settings, PatA/PatB, is shown to challenge this concept. It clearly favors GTP as the energy supply to expel drugs. This preference is correlated to its ability to hydrolyze GTP more efficiently than ATP, as found with PatA/PatB reconstituted in proteoliposomes or nanodiscs. Importantly, the ATP and GTP concentrations are similar in S. pneumoniae supporting the physiological relevance of GTP as the energy source of this bacterial transporter.
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Affiliation(s)
- Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France
| | - Claire Durmort
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
| | - Khadija Mathieu
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France
| | - Benjamin Duchêne
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Sandrine Aros
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - François Fenaille
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - François André
- Laboratoire Stress Oxydant et Détoxication (LSOD), Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Christophe Junot
- CEA, Institut Joliot, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191, Gif-sur-Yvette cedex, France
| | - Thierry Vernet
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
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16
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Collauto A, Mishra S, Litvinov A, Mchaourab HS, Goldfarb D. Direct Spectroscopic Detection of ATP Turnover Reveals Mechanistic Divergence of ABC Exporters. Structure 2017; 25:1264-1274.e3. [PMID: 28712805 DOI: 10.1016/j.str.2017.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/05/2017] [Accepted: 06/15/2017] [Indexed: 12/27/2022]
Abstract
We have applied high-field (W-band) pulse electron-nuclear double resonance (ENDOR) and electron-electron double resonance (ELDOR)-detected nuclear magnetic resonance (EDNMR) to characterize the coordination sphere of the Mn2+ co-factor in the nucleotide binding sites (NBSs) of ABC transporters. MsbA and BmrCD are two efflux transporters hypothesized to represent divergent catalytic mechanisms. Our results reveal distinct coordination of Mn2+ to ATP and transporter residues in the consensus and degenerate NBSs of BmrCD. In contrast, the coordination of Mn2+ at the two NBSs of MsbA is similar, which provides a mechanistic rationale for its higher rate constant of ATP hydrolysis relative to BmrCD. Direct detection of vanadate ion, trapped in a high-energy post-hydrolysis intermediate, further supports the notion of asymmetric hydrolysis by the two NBSs of BmrCD. The integrated spectroscopic approach presented here, which link energy input to conformational dynamics, can be applied to a variety of systems powered by ATP turnover.
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Affiliation(s)
- Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Aleksei Litvinov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel.
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17
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Hassan KA, Fagerlund A, Elbourne LDH, Vörös A, Kroeger JK, Simm R, Tourasse NJ, Finke S, Henderson PJF, Økstad OA, Paulsen IT, Kolstø AB. The putative drug efflux systems of the Bacillus cereus group. PLoS One 2017; 12:e0176188. [PMID: 28472044 PMCID: PMC5417439 DOI: 10.1371/journal.pone.0176188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/06/2017] [Indexed: 12/19/2022] Open
Abstract
The Bacillus cereus group of bacteria includes seven closely related species, three of which, B. anthracis, B. cereus and B. thuringiensis, are pathogens of humans, animals and/or insects. Preliminary investigations into the transport capabilities of different bacterial lineages suggested that genes encoding putative efflux systems were unusually abundant in the B. cereus group compared to other bacteria. To explore the drug efflux potential of the B. cereus group all putative efflux systems were identified in the genomes of prototypical strains of B. cereus, B. anthracis and B. thuringiensis using our Transporter Automated Annotation Pipeline. More than 90 putative drug efflux systems were found within each of these strains, accounting for up to 2.7% of their protein coding potential. Comparative analyses demonstrated that the efflux systems are highly conserved between these species; 70-80% of the putative efflux pumps were shared between all three strains studied. Furthermore, 82% of the putative efflux system proteins encoded by the prototypical B. cereus strain ATCC 14579 (type strain) were found to be conserved in at least 80% of 169 B. cereus group strains that have high quality genome sequences available. However, only a handful of these efflux pumps have been functionally characterized. Deletion of individual efflux pump genes from B. cereus typically had little impact to drug resistance phenotypes or the general fitness of the strains, possibly because of the large numbers of alternative efflux systems that may have overlapping substrate specificities. Therefore, to gain insight into the possible transport functions of efflux systems in B. cereus, we undertook large-scale qRT-PCR analyses of efflux pump gene expression following drug shocks and other stress treatments. Clustering of gene expression changes identified several groups of similarly regulated systems that may have overlapping drug resistance functions. In this article we review current knowledge of the small molecule efflux pumps encoded by the B. cereus group and suggest the likely functions of numerous uncharacterised pumps.
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Affiliation(s)
- Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Annette Fagerlund
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Liam D. H. Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Aniko Vörös
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Jasmin K. Kroeger
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Freiburg, Germany
| | - Roger Simm
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Nicolas J. Tourasse
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Sarah Finke
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Peter J. F. Henderson
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (ABK); (ITP)
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- * E-mail: (ABK); (ITP)
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18
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Leroy M, Piton J, Gilet L, Pellegrini O, Proux C, Coppée JY, Figaro S, Condon C. Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis. EMBO J 2017; 36:1167-1181. [PMID: 28363943 DOI: 10.15252/embj.201796540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 11/09/2022] Open
Abstract
The PIN domain plays a central role in cellular RNA biology and is involved in processes as diverse as rRNA maturation, mRNA decay and telomerase function. Here, we solve the crystal structure of the Rae1 (YacP) protein of Bacillus subtilis, a founding member of the NYN (Nedd4-BP1/YacP nuclease) subfamily of PIN domain proteins, and identify potential substrates in vivo Unexpectedly, degradation of a characterised target mRNA was completely dependent on both its translation and reading frame. We provide evidence that Rae1 associates with the B. subtilis ribosome and cleaves between specific codons of this mRNA in vivo Critically, we also demonstrate translation-dependent Rae1 cleavage of this substrate in a purified translation assay in vitro Multiple lines of evidence converge to suggest that Rae1 is an A-site endoribonuclease. We present a docking model of Rae1 bound to the B. subtilis ribosomal A-site that is consistent with this hypothesis and show that Rae1 cleaves optimally immediately upstream of a lysine codon (AAA or AAG) in vivo.
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Affiliation(s)
- Magali Leroy
- UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Jérémie Piton
- UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Laetitia Gilet
- UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Olivier Pellegrini
- UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Caroline Proux
- Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research Institut Pasteur, Paris, France
| | - Sabine Figaro
- UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Ciarán Condon
- UMR 8261 (CNRS - Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
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19
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Quantification of Detergents Complexed with Membrane Proteins. Sci Rep 2017; 7:41751. [PMID: 28176812 PMCID: PMC5297245 DOI: 10.1038/srep41751] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/23/2016] [Indexed: 01/20/2023] Open
Abstract
Most membrane proteins studies require the use of detergents, but because of the lack of a general, accurate and rapid method to quantify them, many uncertainties remain that hamper proper functional and structural data analyses. To solve this problem, we propose a method based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) that allows quantification of pure or mixed detergents in complex with membrane proteins. We validated the method with a wide variety of detergents and membrane proteins. We automated the process, thereby allowing routine quantification for a broad spectrum of usage. As a first illustration, we show how to obtain information of the amount of detergent in complex with a membrane protein, essential for liposome or nanodiscs reconstitutions. Thanks to the method, we also show how to reliably and easily estimate the detergent corona diameter and select the smallest size, critical for favoring protein-protein contacts and triggering/promoting membrane protein crystallization, and to visualize the detergent belt for Cryo-EM studies.
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20
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Reynolds LJ, Roberts AP, Anjum MF. Efflux in the Oral Metagenome: The Discovery of a Novel Tetracycline and Tigecycline ABC Transporter. Front Microbiol 2016; 7:1923. [PMID: 27999567 PMCID: PMC5138185 DOI: 10.3389/fmicb.2016.01923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance in human bacterial pathogens and commensals is threatening our ability to treat infections and conduct common medical procedures. As novel antibiotics are discovered and marketed it is important that we understand how resistance to them may arise and know what environments may act as reservoirs for such resistance genes. In this study a tetracycline and tigecycline resistant clone was identified by screening a human saliva metagenomic library in Escherichia coli EPI300 on agar containing 5 μg/ml tetracycline. Sequencing of the DNA insert present within the tetracycline resistant clone revealed it to contain a 7,765 bp fragment harboring novel ABC half transporter genes, tetAB(60). Mutagenesis studies performed on these genes confirmed that they were responsible for the tetracycline and tigecycline resistance phenotypes. Growth studies performed using E. coli EPI300 clones that harbored either the wild type, the mutated, or none of these genes indicated that there was a fitness cost associated with presence of these genes, with the isolate harboring both genes exhibiting a significantly slower growth than control strains. Given the emergence of E. coli strains that are sensitive only to tigecycline and doxycycline it is concerning that such a resistance mechanism has been identified in the human oral cavity.
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Affiliation(s)
- Liam J Reynolds
- Department of Microbial Diseases, UCL Eastman Dental Institute, Faculty of Medical Sciences, University College LondonLondon, UK; Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
| | - Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, Faculty of Medical Sciences, University College London London, UK
| | - Muna F Anjum
- Department of Microbial Diseases, UCL Eastman Dental Institute, Faculty of Medical Sciences, University College LondonLondon, UK; Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
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21
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Reilman E, Mars RAT, van Dijl JM, Denham EL. The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism. Nucleic Acids Res 2014; 42:11393-407. [PMID: 25217586 PMCID: PMC4191407 DOI: 10.1093/nar/gku832] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of particular drug transporters in response to antibiotic pressure is a critical element in the development of bacterial multidrug resistance, and represents a serious concern for human health. To obtain a better understanding of underlying regulatory mechanisms, we have dissected the transcriptional activation of the ATP-binding cassette (ABC) transporter BmrC/BmrD of the Gram-positive model bacterium Bacillus subtilis. By using promoter-GFP fusions and live cell array technology, we demonstrate a temporally controlled transcriptional activation of the bmrCD genes in response to antibiotics that target protein synthesis. Intriguingly, bmrCD expression only occurs during the late-exponential and stationary growth stages, irrespective of the timing of the antibiotic challenge. We show that this is due to tight transcriptional control by the transition state regulator AbrB. Moreover, our results show that the bmrCD genes are co-transcribed with bmrB (yheJ), a small open reading frame immediately upstream of bmrC that harbors three alternative stem-loop structures. These stem-loops are apparently crucial for antibiotic-induced bmrCD transcription. Importantly, the antibiotic-induced bmrCD expression requires translation of bmrB, which implies that BmrB serves as a regulatory leader peptide. Altogether, we demonstrate for the first time that a ribosome-mediated transcriptional attenuation mechanism can control the expression of a multidrug ABC transporter.
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Affiliation(s)
- Ewoud Reilman
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, P.O. box 30001, 9700 RB Groningen, the Netherlands
| | - Ruben A T Mars
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, P.O. box 30001, 9700 RB Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, P.O. box 30001, 9700 RB Groningen, the Netherlands
| | - Emma L Denham
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, P.O. box 30001, 9700 RB Groningen, the Netherlands
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22
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Laursen MF, Bahl MI, Licht TR, Gram L, Knudsen GM. A single exposure to a sublethal pediocin concentration initiates a resistance-associated temporal cell envelope and general stress response inListeria monocytogenes. Environ Microbiol 2014; 17:1134-51. [DOI: 10.1111/1462-2920.12534] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 06/08/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Martin F. Laursen
- Department of Systems Biology; Technical University of Denmark; DK-2800 Kongens Lyngby Denmark
- National Food Institute; Technical University of Denmark; DK-2860 Søborg Denmark
| | - Martin I. Bahl
- National Food Institute; Technical University of Denmark; DK-2860 Søborg Denmark
| | - Tine R. Licht
- National Food Institute; Technical University of Denmark; DK-2860 Søborg Denmark
| | - Lone Gram
- Department of Systems Biology; Technical University of Denmark; DK-2800 Kongens Lyngby Denmark
| | - Gitte M. Knudsen
- Department of Systems Biology; Technical University of Denmark; DK-2800 Kongens Lyngby Denmark
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Mishra S, Verhalen B, Stein RA, Wen PC, Tajkhorshid E, Mchaourab HS. Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter. eLife 2014; 3:e02740. [PMID: 24837547 PMCID: PMC4046567 DOI: 10.7554/elife.02740] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Multidrug ATP binding cassette (ABC) exporters are ubiquitous ABC transporters that extrude cytotoxic molecules across cell membranes. Despite recent progress in structure determination of these transporters, the conformational motion that transduces the energy of ATP hydrolysis to the work of substrate translocation remains undefined. Here, we have investigated the conformational cycle of BmrCD, a representative of the heterodimer family of ABC exporters that have an intrinsically impaired nucleotide binding site. We measured distances between pairs of spin labels monitoring the movement of the nucleotide binding (NBD) and transmembrane domains (TMD). The results expose previously unobserved structural intermediates of the NBDs arising from asymmetric configuration of catalytically inequivalent nucleotide binding sites. The two-state transition of the TMD, from an inward- to an outward-facing conformation, is driven exclusively by ATP hydrolysis. These findings provide direct evidence of divergence in the mechanism of ABC exporters.DOI: http://dx.doi.org/10.7554/eLife.02740.001.
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Affiliation(s)
- Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Brandy Verhalen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Po-Chao Wen
- Department of Biochemistry, College of Medicine, University of Illinois, Urbana, United States Center for Biophysics and Computational Biology, University of Illinois, Urbana, United States The Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Unites States
| | - Emad Tajkhorshid
- Department of Biochemistry, College of Medicine, University of Illinois, Urbana, United States Center for Biophysics and Computational Biology, University of Illinois, Urbana, United States The Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Unites States
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
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24
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Bara R, Zerfass I, Aly AH, Goldbach-Gecke H, Raghavan V, Sass P, Mándi A, Wray V, Polavarapu PL, Pretsch A, Lin W, Kurtán T, Debbab A, Brötz-Oesterhelt H, Proksch P. Atropisomeric dihydroanthracenones as inhibitors of multiresistant Staphylococcus aureus. J Med Chem 2013; 56:3257-72. [PMID: 23534483 DOI: 10.1021/jm301816a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Two bisdihydroanthracenone atropodiastereomeric pairs, including homodimeric flavomannin A (1) and the previously unreported flavomannin B (2), two new unsymmetrical dimers (3 and 4), and two new mixed dihydroanthracenone/anthraquinone dimers (5 and 6) were isolated from Talaromyces wortmannii , an endophyte of Aloe vera . The structures of 2-6 were elucidated by extensive NMR and mass spectrometric analyses. The axial chirality of the biaryls was determined using TDDFT ECD and VCD calculations, the combination of which however did not allow the assignment of the central chirality elements of 1. The compounds exhibited antibacterial activity against Staphylococcus aureus , including (multi)drug-resistant clinical isolates. Reporter gene analyses indicated induction of the SOS response for some of the derivatives, suggesting interference with DNA structure or metabolism. Fluorescence microscopy demonstrated defective segregation of the bacterial chromosome and DNA degradation. Notably, the compounds showed no cytotoxic activity, encouraging their further evaluation as potential starting points for antibacterial drug development.
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Affiliation(s)
- Robert Bara
- Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, Geb. 26.23, 40225 Düsseldorf, Germany
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25
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Boncoeur E, Durmort C, Bernay B, Ebel C, Di Guilmi AM, Croizé J, Vernet T, Jault JM. PatA and PatB Form a Functional Heterodimeric ABC Multidrug Efflux Transporter Responsible for the Resistance of Streptococcus pneumoniae to Fluoroquinolones. Biochemistry 2012; 51:7755-65. [DOI: 10.1021/bi300762p] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Emilie Boncoeur
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
| | - Claire Durmort
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
| | - Benoît Bernay
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
| | - Christine Ebel
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
| | - Anne Marie Di Guilmi
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
| | - Jacques Croizé
- Unité de bactériologie, CHU la Tronche, Grenoble, France
| | - Thierry Vernet
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
| | - Jean-Michel Jault
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale,
Grenoble, France, CNRS, Institut de Biologie
Structurale, Grenoble, France, and CEA,
Institut de Biologie Structurale, Grenoble, France
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26
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Warburton PJ, Ciric L, Lerner A, Seville LA, Roberts AP, Mullany P, Allan E. TetAB46, a predicted heterodimeric ABC transporter conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity. J Antimicrob Chemother 2012; 68:17-22. [PMID: 22941900 PMCID: PMC3522447 DOI: 10.1093/jac/dks351] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objectives To identify the genes responsible for tetracycline resistance in a strain of Streptococcus australis isolated from pooled saliva from healthy volunteers in France. S. australis is a viridans Streptococcus, originally isolated from the oral cavity of children in Australia, and subsequently reported in the lungs of cystic fibrosis patients and as a cause of invasive disease in an elderly patient. Methods Agar containing 2 mg/L tetracycline was used for the isolation of tetracycline-resistant organisms. A genomic library in Escherichia coli was used to isolate the tetracycline resistance determinant. In-frame deletions and chromosomal repair were used to confirm function. Antibiotic susceptibility was determined by agar dilution and disc diffusion assay. Results The tetracycline resistance determinant from S. australis FRStet12 was isolated from a genomic library in E. coli and DNA sequencing showed two open reading frames predicted to encode proteins with similarity to multidrug resistance-type ABC transporters. Both genes were required for tetracycline resistance (to both the naturally occurring and semi-synthetic tetracyclines) and they were designated tetAB(46). Conclusions This is the first report of a predicted ABC transporter conferring tetracycline resistance in a member of the oral microbiota.
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Affiliation(s)
- Philip J Warburton
- Research Department of Microbial Diseases, UCL Eastman Dental Institute, 256 Gray's Inn Road, University College London, London WC1X 8LD, UK
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Identification of MrtAB, an ABC transporter specifically required for Yersinia pseudotuberculosis to colonize the mesenteric lymph nodes. PLoS Pathog 2012; 8:e1002828. [PMID: 22876175 PMCID: PMC3410872 DOI: 10.1371/journal.ppat.1002828] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 06/15/2012] [Indexed: 12/26/2022] Open
Abstract
A highly conserved virulence plasmid encoding a type III secretion system is shared by the three Yersinia species most pathogenic for mammals. Although factors encoded on this plasmid enhance the ability of Yersinia to thrive in their mammalian hosts, the loss of this virulence plasmid does not eliminate growth or survival in host organs. Most notably, yields of viable plasmid-deficient Yersinia pseudotuberculosis (Yptb) are indistinguishable from wild-type Yptb within mesenteric lymph nodes. To identify chromosomal virulence factors that allow for plasmid-independent survival during systemic infection of mice, we generated transposon insertions in plasmid-deficient Yptb, and screened a library having over 20,000 sequence-identified insertions. Among the previously uncharacterized loci, insertions in mrtAB, an operon encoding an ABC family transporter, had the most profound phenotype in a plasmid-deficient background. The absence of MrtAB, however, had no effect on growth in the liver and spleen of a wild type strain having an intact virulence plasmid, but caused a severe defect in colonization of the mesenteric lymph nodes. Although this result is consistent with lack of expression of the type III secretion system by Wt Yptb in the mesenteric lymph nodes, a reporter for YopE indicated that expression of the system was robust. We demonstrate that the ATPase activity of MrtB is required for growth in mice, indicating that transport activity is required for virulence. Indeed, MrtAB appears to function as an efflux pump, as the ATPase activity enhances resistance to ethidium bromide while increasing sensitivity to pyocyanin, consistent with export across the inner membrane.
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28
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Casabona MG, Silverman JM, Sall KM, Boyer F, Couté Y, Poirel J, Grunwald D, Mougous JD, Elsen S, Attree I. An ABC transporter and an outer membrane lipoprotein participate in posttranslational activation of type VI secretion in Pseudomonas aeruginosa. Environ Microbiol 2012; 15:471-86. [PMID: 22765374 DOI: 10.1111/j.1462-2920.2012.02816.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pseudomonas aeruginosa is capable of injecting protein toxins into other bacterial cells through one of its three type VI secretion systems (T6SSs). The activity of this T6SS is tightly regulated on the posttranslational level by phosphorylation-dependent and -independent pathways. The phosphorylation-dependent pathway consists of a Threonine kinase/phosphatase pair (PpkA/PppA) that acts on a forkhead domain-containing protein, Fha1, and a periplasmic protein, TagR, that positively regulates PpkA. In the present work, we biochemically and functionally characterize three additional proteins of the phosphorylation-dependent regulatory cascade that controls T6S activation: TagT, TagS and TagQ. We show that similar to TagR, these proteins act upstream of the PpkA/PppA checkpoint and influence phosphorylation of Fha1 and, apparatus assembly and effector export. Localization studies demonstrate that TagQ is an outer membrane lipoprotein and TagR is associated with the outer membrane. Consistent with their homology to lipoprotein outer membrane localization (Lol) components, TagT and TagS form a stable inner membrane complex with ATPase activity. However, we find that outer membrane association of T6SS lipoproteins TagQ and TssJ1, and TagR, is unaltered in a ΔtagTS background. Notably, we found that TagQ is indispensible for anchoring of TagR to the outer membrane fraction. As T6S-dependent fitness of P. aeruginosa requires TagT, S, R and Q, we conclude that these proteins likely participate in a trans-membrane signalling pathway that promotes H1-T6SS activity under optimal environmental conditions.
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Affiliation(s)
- Maria G Casabona
- INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble, France
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29
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Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation. Nat Struct Mol Biol 2012; 19:395-402. [PMID: 22447242 DOI: 10.1038/nsmb.2267] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/17/2012] [Indexed: 11/08/2022]
Abstract
ATP-binding cassette (ABC) transporters shuttle a wide variety of molecules across cell membranes by alternating between inward- and outward-facing conformations, harnessing the energy of ATP binding and hydrolysis at their nucleotide binding domains (NBDs). Here we present the 2.9-Å crystal structure of the heterodimeric ABC transporter TM287-TM288 (TM287/288) from Thermotoga maritima in its inward-facing state. In contrast to previous studies, we found that the NBDs only partially separate, remaining in contact through an interface involving conserved motifs that connect the two ATP hydrolysis sites. We observed AMP-PNP binding to the degenerate catalytic site, which deviates from the consensus sequence in the same positions as the eukaryotic homologs CFTR and TAP1-TAP2 (TAP1/2). The TM287/288 structure provides unprecedented insights into the mechanism of heterodimeric ABC exporters and will enable future studies on this large transporter superfamily.
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30
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Optimized purification of a heterodimeric ABC transporter in a highly stable form amenable to 2-D crystallization. PLoS One 2011; 6:e19677. [PMID: 21602923 PMCID: PMC3094339 DOI: 10.1371/journal.pone.0019677] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 04/06/2011] [Indexed: 12/24/2022] Open
Abstract
Optimized protocols for achieving high-yield expression, purification and reconstitution of membrane proteins are required to study their structure and function. We previously reported high-level expression in Escherichia coli of active BmrC and BmrD proteins from Bacillus subtilis, previously named YheI and YheH. These proteins are half-transporters which belong to the ABC (ATP-Binding Cassette) superfamily and associate in vivo to form a functional transporter able to efflux drugs. In this report, high-yield purification and functional reconstitution were achieved for the heterodimer BmrC/BmrD. In contrast to other detergents more efficient for solubilizing the transporter, dodecyl-ß-D-maltoside (DDM) maintained it in a drug-sensitive and vanadate-sensitive ATPase-competent state after purification by affinity chromatography. High amounts of pure proteins were obtained which were shown either by analytical ultracentrifugation or gel filtration to form a monodisperse heterodimer in solution, which was notably stable for more than one month at 4°C. Functional reconstitution using different lipid compositions induced an 8-fold increase of the ATPase activity (kcat∼5 s−1). We further validated that the quality of the purified BmrC/BmrD heterodimer is suitable for structural analyses, as its reconstitution at high protein densities led to the formation of 2-D crystals. Electron microscopy of negatively stained crystals allowed the calculation of a projection map at 20 Å resolution revealing that BmrC/BmrD might assemble into oligomers in a lipidic environment.
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31
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Matar-Merheb R, Rhimi M, Leydier A, Huché F, Galián C, Desuzinges-Mandon E, Ficheux D, Flot D, Aghajari N, Kahn R, Di Pietro A, Jault JM, Coleman AW, Falson P. Structuring detergents for extracting and stabilizing functional membrane proteins. PLoS One 2011; 6:e18036. [PMID: 21483854 PMCID: PMC3069034 DOI: 10.1371/journal.pone.0018036] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 02/22/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Membrane proteins are privileged pharmaceutical targets for which the development of structure-based drug design is challenging. One underlying reason is the fact that detergents do not stabilize membrane domains as efficiently as natural lipids in membranes, often leading to a partial to complete loss of activity/stability during protein extraction and purification and preventing crystallization in an active conformation. METHODOLOGY/PRINCIPAL FINDINGS Anionic calix[4]arene based detergents (C4Cn, n=1-12) were designed to structure the membrane domains through hydrophobic interactions and a network of salt bridges with the basic residues found at the cytosol-membrane interface of membrane proteins. These compounds behave as surfactants, forming micelles of 5-24 nm, with the critical micellar concentration (CMC) being as expected sensitive to pH ranging from 0.05 to 1.5 mM. Both by 1H NMR titration and Surface Tension titration experiments, the interaction of these molecules with the basic amino acids was confirmed. They extract membrane proteins from different origins behaving as mild detergents, leading to partial extraction in some cases. They also retain protein functionality, as shown for BmrA (Bacillus multidrug resistance ATP protein), a membrane multidrug-transporting ATPase, which is particularly sensitive to detergent extraction. These new detergents allow BmrA to bind daunorubicin with a Kd of 12 µM, a value similar to that observed after purification using dodecyl maltoside (DDM). They preserve the ATPase activity of BmrA (which resets the protein to its initial state after drug efflux) much more efficiently than SDS (sodium dodecyl sulphate), FC12 (Foscholine 12) or DDM. They also maintain in a functional state the C4Cn-extracted protein upon detergent exchange with FC12. Finally, they promote 3D-crystallization of the membrane protein. CONCLUSION/SIGNIFICANCE These compounds seem promising to extract in a functional state membrane proteins obeying the positive inside rule. In that context, they may contribute to the membrane protein crystallization field.
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Affiliation(s)
- Rima Matar-Merheb
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
| | - Moez Rhimi
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
- Laboratoire de BioCristallographie et Biologie Structurale des Cibles Thérapeutiques, Université Lyon 1, Univ Lyon; CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Lyon, France
| | | | - Frédéric Huché
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
- Laboratoire de BioCristallographie et Biologie Structurale des Cibles Thérapeutiques, Université Lyon 1, Univ Lyon; CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Lyon, France
| | - Carmen Galián
- CNRS/CEA/Université Joseph Fourier, Institut de Biologie Structurale, Grenoble, France
| | - Elodie Desuzinges-Mandon
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
| | - Damien Ficheux
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
| | - David Flot
- European Synchrotron Radiation Facility, BP 220, Grenoble, France
| | - Nushin Aghajari
- Laboratoire de BioCristallographie et Biologie Structurale des Cibles Thérapeutiques, Université Lyon 1, Univ Lyon; CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Lyon, France
| | - Richard Kahn
- CNRS/CEA/Université Joseph Fourier, Institut de Biologie Structurale, Grenoble, France
| | - Attilio Di Pietro
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
| | - Jean-Michel Jault
- CNRS/CEA/Université Joseph Fourier, Institut de Biologie Structurale, Grenoble, France
| | - Anthony W. Coleman
- Laboratoire des Multimatériaux et Interfaces, UMR 5615 CNRS/Université de Lyon 1, Lyon, France
| | - Pierre Falson
- CNRS, Drug Resistance Mechanism and Modulation Laboratory, Ligue labeled team 2009, Lyon, France
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32
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Zutz A, Hoffmann J, Hellmich UA, Glaubitz C, Ludwig B, Brutschy B, Tampé R. Asymmetric ATP hydrolysis cycle of the heterodimeric multidrug ABC transport complex TmrAB from Thermus thermophilus. J Biol Chem 2010; 286:7104-15. [PMID: 21190941 DOI: 10.1074/jbc.m110.201178] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ATP-binding cassette (ABC) systems translocate a wide range of solutes across cellular membranes. The thermophilic gram-negative eubacterium Thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 ABC proteins, which are largely uncharacterized. Here, we functionally analyzed the first two and only ABC half-transporters of the hyperthermophilic bacterium, TmrA and TmrB. The ABC system mediates uptake of the drug Hoechst 33342 in inside-out oriented vesicles that is inhibited by verapamil. TmrA and TmrB form a stable heterodimeric complex hydrolyzing ATP with a K(m) of 0.9 mm and k(cat) of 9 s(-1) at 68 °C. Two nucleotides can be trapped in the heterodimeric ABC complex either by vanadate or by mutation inhibiting ATP hydrolysis. Nucleotide trapping requires permissive temperatures, at which a conformational ATP switch is possible. We further demonstrate that the canonic glutamate 523 of TmrA is essential for rapid conversion of the ATP/ATP-bound complex into its ADP/ATP state, whereas the corresponding aspartate in TmrB (Asp-500) has only a regulatory role. Notably, exchange of this single noncanonic residue into a catalytic glutamate cannot rescue the function of the E523Q/D500E complex, implicating a built-in asymmetry of the complex. However, slow ATP hydrolysis in the newly generated canonic site (D500E) strictly depends on the formation of a posthydrolysis state in the consensus site, indicating an allosteric coupling of both active sites.
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Affiliation(s)
- Ariane Zutz
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, D-60438 Frankfurt, Germany
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